9 has a bunch of them. 2 gets a bunch ((which makes it all the more heart-wrenching when he dies, and to rub salt on the wound, gets turned into a puppet for The Seamstress * shiver* )) and 5 gets a few. One when they were together: 5 and 9 had just come to save 2, and after they initially thought 2 was dead, 5 had his hand on 2's shoulder and 2 put his hand on 5's with a gentle "I knew you'd come." It's made even sweeter with 5's soft "My love!" right when he realized that 2 was still alive and kicking. And then there was 1's Heroic Sacrifice and his last interaction with 9 after his death...
It's debatable on whether he says "I thought" or "My love", but the moment still cements the fact that the two are the best of best friends.
'Nother 2 example: him running over to 7 and glomping her after she kills the Cat Beast. She stands there, stunned, for a moment or two, the hugs him back.
The scene where everyone relaxes while "Over the Rainbow" plays on the old record player.
Also, 9's first meeting with 2. "Friend? Friend"
When the final shot revealed that the raindrops were teeming with living microbes. After an entire film's worth of devastated landscape, it was the crown on the heartwarming of the souls' release.
The last two lines between 9 and 7 during that final shot.
7: What happens now?
9: I'm not sure exactly. But this world is ours now. It's what we make of it.
1's final gesture to 9 after his soul is released from the device. A simple pat on the shoulder, a smile, and a nod.